I dont' think you can.
From time to time I have this situation and I just accept that there will be some extra costs for me.
Then after packaging and determining the actual postage costs, I go to Paypal and REFUND all or part of the shipping on the items.
So if someone buys two items that I normally charge $3.99 to ship, but they can be shipped together for $4.50, I will choose one of the items and REFUND $0.51 from their payment.
I still have to pay the two PP fees, and a 50 cent refund seems stingy, but it is appreciated.